.. _exercises2018:

NEURON Course Exercises
=======================

These exercises are adapted from the 2018 NEURON summer course given in Atlanta, Georgia.

1.
    :ref:`intro_to_gui`

        * Lipid bilayer model

2.    
  :ref:`interactive_modeling`

        * Squid axon model

3.    
   :ref:`the_cellbuilder`

        * Constructing a ball and stick model, saving session files

4.    
    :ref:`using_morphometric_data`

        * The Import3D tool
    
5.
    :ref:`neuron_scripting_exercises`
    
6.
    :ref:`using_nmodl_files`

        * Single compartment model with HHk mechanism

7.    
    :ref:`using_modeldb_and_modelview`

        * Neuroinformatics tools for finding and understanding models

8.    
    :ref:`rxd_exercises`

9.    
    :ref:`specifying_inhomogeneous_channel_distributions_with_the_cellbuilder`

10.    
    :ref:`custom_initialization`
    
11.
    :ref:`introduction_to_the_linear_circuit`

        * A two-electrode voltage clamp
    
12.
    :ref:`state_and_parameter_discontinuities`
    
13.
    :ref:`Bulletin board parallelization <batch_runs_with_bulletin_board_parallelization>`

        * Speed up embarrassingly parallel tasks
    
14.
    :ref:`hoc_exercises`

        * Introduction to the HOC programming language
    
15.
    :ref:`multithread_parallelization`
    
16.
    :ref:`Networks: discrete event simulations with artificial cells <intro_to_the_network_builder>`

        * Introduction to the Network Builder
    
17.
    :ref:`Networks: continuous simulation of nets with biophysical model cells <network_ready_cells_from_the_cellbuilder>`

        * Network ready cells from the CellBuilder
    
18.
    :ref:`Hopfield-Brody network in Python <hopfield_brody_network_in_python>`
    
19.
    :ref:`MPI Parallelization <mpi_parallelization>`
    
20.
    :ref:`using_nsg_portal`
    
21.
    :ref:`numerical_methods_exercises`
    
22.
    :ref:`electrotonic_analysis`

.. toctree::
    :hidden:

    intro_to_gui.rst
    interactive_modeling.rst
    the_cellbuilder.rst
    neuron_scripting_exercises.rst
    using_morphometric_data
    using_nmodl_files.rst
    using_modeldb_and_modelview.rst
    rxd_exercises.rst
    specifying_inhomogeneous_channel_dis.rst
    custom-initialization.rst
    introduction_to_the_linear_circuit.rst
    state_and_parameter_discontinuities.rst
    batch_runs_with_bulletin_board.rst
    hoc_exercises.rst
    multithread_parallelization.rst
    intro_to_the_network_builder.rst
    network_ready_cells_from_the_cellb.rst
    hopfield_brody_network_in_python.rst
    mpi_parallelization.rst
    using_nsg_portal.rst
    numerical-methods-exercises.rst
    electrotonic_analysis.rst
    
